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peakabif

Extraction of Peak locations, Heights and Surfaces from ABIF data

Description

Simple peak location for data imported with the read.abif function using cubic spline interpolation.

Usage

peakabif(abifdata, 
  chanel, 
  npeak, 
  thres = 400/yscale, 
  fig = TRUE,
  chanel.names = c(1:4,105),
  DATA = paste("DATA", chanel.names[chanel], sep = "."),
  tmin = 1/tscale,
  tmax = abifdata$Data[["SCAN.1"]]/tscale,
  tscale = 1000, 
  yscale = 1000,
  irange = (tmin*tscale):(tmax*tscale),
  y = abifdata$Data[[DATA]][irange]/yscale,
  method = "monoH.FC",
  maxrfu = 1000,
  ...)

Arguments

abifdata

the result returned by read.abif
chanel

the dye number
npeak

the expected number of peaks
thres

scaled threshold value
fig

logical: should localized peaks be plotted
chanel.names

numbers extensions used for the DATA
DATA

names of the DATA components
tmin

scaled starting time for the time axis
tmax

scaled ending time for the time axis
tscale

scale factor for the time axis
yscale

scale factor for the y-axis (RFU)
irange

indices of data to be plotted
y

values used for the y-axis
method

method to be used by splinefun
maxrfu

argument passed to baselineabif
...

arguments forwarded to plot

Value

Returns invisibly a list with the unscaled values for the locations of peaks, heights of peaks and surfaces of peaks and baseline estimate. The peak location are in datapoint units, that is an integer starting at 1 for the first experimental point, 2 for the second experimental point, etc. However, due to interpolation between points the estimated peak location is usually not an integer.

Author(s)

J.R. Lobry

References

citation("seqinr")

See Also

function read.abif to import files in ABIF format, plotabif to plot them, data gs500liz for internal size standards, data identifiler for allele names in the allelic ladder, data JLO for an example of an individual sample file, data ECH for an example of an allelic lader.

Examples

data(JLO)
JLO.maxis <- peakabif(JLO, 5, npeak = 14, tmin = 2.7, thres = 0.1)$maxis
seqinr

Biological Sequences Retrieval and Analysis

v4.2-16
GPL (>= 2)
Authors
Delphine Charif [aut], Olivier Clerc [ctb], Carolin Frank [ctb], Jean R. Lobry [aut, cph], Anamaria Necşulea [ctb], Leonor Palmeira [ctb], Simon Penel [cre], Guy Perrière [ctb]
Initial release
2022-05-19

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